def methyl_protons(file):
obconversion = OBConversion()
obconversion.SetInFormat("sdf")
obmol = OBMol()
obconversion.ReadFile(obmol, file)
methyl_protons = []
for atom in OBMolAtomIter(obmol):
count = 0
nbrprotons = []
for NbrAtom in OBAtomAtomIter(atom):
if (atom.GetAtomicNum() == 6) & (NbrAtom.GetAtomicNum() == 1):
l = NbrAtom.GetIndex()
count += 1
nbrprotons.append('H' + str(l + 1))
if count == 3:
methyl_protons.append(nbrprotons)
return methyl_protons
def remove_labile_protons(sdffile, lbls, shifts):
f = sdffile.split('.sdf')[0] + '.sdf'
obconversion = OBConversion()
obconversion.SetInFormat("sdf")
obmol = OBMol()
obconversion.ReadFile(obmol, f)
CI = []
for atom in OBMolAtomIter(obmol):
if atom.GetAtomicNum() == 1:
for NbrAtom in OBAtomAtomIter(atom):
if (NbrAtom.GetAtomicNum() == 8):
CI.append('H' + str(atom.GetIndex() + 1))
#remove these carbons
for C in CI:
ind = lbls.index(C)
lbls.remove(C)
for l in shifts:
l.pop(ind)
return lbls, shifts
def Karplus(f, inputformat):
obconversion = OBConversion()
obconversion.SetInFormat(inputformat)
obmol = OBMol()
obconversion.ReadFile(obmol, f)
obmol.ConnectTheDots()
obmol.Kekulize()
DihedralHs = []
for atom in OBMolAtomIter(obmol):
if atom.GetAtomicNum() == 1:
DihedNeighbours = GetDihedralHs(atom)
if DihedNeighbours != 0:
DihedralHs.append([atom.GetIdx()] + DihedNeighbours)
if len(DihedralHs) == 0:
print("No dihedral protons found, Karplus J value prediction " + \
"impossible, quitting.")
quit()
Jmatrix, Jlabels = CalcJMatrix(obmol, DihedralHs)
Jlabels = [str(x) for x in Jlabels]
return Jmatrix, Jlabels
def RestoreNumsSDF(f, fold, AuxInfo):
#Read molecule from file
obconversion = OBConversion()
obconversion.SetInFormat("sdf")
obmol = OBMol()
obconversion.ReadFile(obmol, f)
#Get the atoms Hs are connected to
oldHcons = GetHcons(fold)
#translate the H connected atoms to the new numbering system
amap = GetInchiRenumMap(AuxInfo)
for i in range(0, len(oldHcons)):
oldHcons[i][1] = amap.index(oldHcons[i][1]) + 1
newHcons = []
temp = []
i = 0
for atom in OBMolAtomIter(obmol):
idx = atom.GetIdx()
anum = atom.GetAtomicNum()
#If atom is hydrogen, check what it is connected to
if anum == 1:
for NbrAtom in OBAtomAtomIter(atom):
newHcons.append([idx, NbrAtom.GetIdx()])
#Pick the temporary atom
temp.append(atom)
for i in range(0, len(newHcons)):
conatom = newHcons[i][1]
for b in range(0, len(oldHcons)):
if conatom == oldHcons[b][1]:
amap.append(oldHcons[b][0])
#remove the number, so that it doesn't get added twice
oldHcons[b][1] = 0
newmol = OBMol()
added = []
for i in range(1, len(amap) + 1):
newn = amap.index(i)
newmol.AddAtom(temp[newn])
added.append(newn)
#Final runthrough to check that all atoms have been added,
#tautomeric protons can be missed. If tautomeric proton tracking
#is implemented this can be removed
for i in range(0, len(temp)):
if not i in added:
newmol.AddAtom(temp[i])
#Restore the bonds
newmol.ConnectTheDots()
newmol.PerceiveBondOrders()
#Write renumbered molecule to file
obconversion.SetOutFormat("sdf")
obconversion.WriteFile(newmol, f)
def GetHcons(f):
obconversion = OBConversion()
obconversion.SetInFormat("sdf")
obmol = OBMol()
obconversion.ReadFile(obmol, f)
Hcons = []
for atom in OBMolAtomIter(obmol):
idx = atom.GetIdx()
anum = atom.GetAtomicNum()
if anum == 1:
for NbrAtom in OBAtomAtomIter(atom):
Hcons.append([idx, NbrAtom.GetIdx()])
return Hcons
def labile_protons(file):
obconversion = OBConversion()
obconversion.SetInFormat("sdf")
obmol = OBMol()
obconversion.ReadFile(obmol, file)
count = 0
for atom in OBMolAtomIter(obmol):
for NbrAtom in OBAtomAtomIter(atom):
if (atom.GetAtomicNum() == 8) & (NbrAtom.GetAtomicNum() == 1):
count += 1
return count
def mol_fragments(mole,outfile):
obconv = OBConversion()
obconv.SetOutFormat("xyz")
c = 1
for atom, exp,dft,diff in zip(OBMolAtomIter(mole)):
# if this is a carbon atom start a breadth first search for other carbon atoms with depth specified
# create a new mol instance
new_mol = OBMol()
# add this atom
# new_mol.AddAtom(atom)
fragment_ind = []
l = atom.GetIndex()
fragment_ind.append(l)
# for iteration depth radius
old_queue = [atom]
for iteration in range(0, 3):
new_queue = []
for a in old_queue:
for atom2 in OBAtomAtomIter(a):
i = atom2.GetIndex()
# if the atom has not been seen before add it to the fragment ind list and to the new molecule
if i not in fragment_ind:
new_queue.append(atom2)
fragment_ind.append(i)
# new_mol.AddAtom(atom2)
old_queue = copy.copy(new_queue)
fragment_ind = [fragment_ind[0]] + sorted(fragment_ind[1:])
for i in fragment_ind:
for a in OBMolAtomIter(mole):
if a.GetIndex() == i:
new_mol.AddAtom(a)
f = open(outfile + "frag" + str(l).zfill(3) + ".xyz", "w+")
f.write(str(new_mol.NumAtoms()) + "\n\n")
i = 0
for atom in OBMolAtomIter(new_mol):
f.write(atom.GetType()[0] + " " + str(atom.GetX()) + " " + str(atom.GetY()) + " " + str(
atom.GetZ()) + "\n")
i+=1
f.close()
c += 1